I will make a quick overview of the quality of the integration of the Liver 2 week deletion plot. First I will plot the starting UMAP plot we got from Carlos of Liver 20Jan21
Carlos_UMAP
Carlos_UMAP_New_Clustering
Now moving onto the plots I produced with the integrated samples. Lets start with the 7 dimensions plot. AV zonation takes the croissant shape, meaning the clear spread across the plot is lost.
I also include Carlos’ Clustering done with the previous 4 conditions, so you can look at the spread.
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 5707
## Number of edges: 173720
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8840
## Number of communities: 7
## Elapsed time: 0 seconds
Moving onto the target genes.
I saw that with 6 dimensions I was able to keep the AV zonation, however the plot looked a bit messier
I also include Carlos’ Clustering done with the previous 4 conditions, so you can look at the spread.
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 5707
## Number of edges: 169683
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8848
## Number of communities: 7
## Elapsed time: 0 seconds